Single cell type - PTCD3 - The Human Protein Atlas

PTCD3

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GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	PTCD3
Gene descriptionⁱ Full gene name according to HGNC.	Pentatricopeptide repeat domain 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Ribosomal proteins
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Cardiomyocytes - Muscle contraction (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Cell type enhanced (Cardiomyocytes)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.32
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Low cell type specificity
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types RNA single cell type specificity: Cell type enhanced (Cardiomyocytes)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

PTCD3 is part of cluster 68 Cardiomyocytes - Muscle contraction with confidenceⁱ 1
262 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
GPD1L	Glycerol-3-phosphate dehydrogenase 1 like	0.5632	68
AGL	Amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	0.5611	2
PKIA	CAMP-dependent protein kinase inhibitor alpha	0.5194	68
ATP5F1A	ATP synthase F1 subunit alpha	0.5052	39
NDUFS1	NADH:ubiquinone oxidoreductase core subunit S1	0.4939	68
TARS2	Threonyl-tRNA synthetase 2, mitochondrial	0.4806	24
TIMM21	Translocase of inner mitochondrial membrane 21	0.4801	68
HSPA9	Heat shock protein family A (Hsp70) member 9	0.4703	80
SDHA	Succinate dehydrogenase complex flavoprotein subunit A	0.4699	68
ELAC2	ElaC ribonuclease Z 2	0.4683	24
PFKM	Phosphofructokinase, muscle	0.4604	68
ABCB7	ATP binding cassette subfamily B member 7	0.4597	39
ATP5PD	ATP synthase peripheral stalk subunit d	0.4563	68
NEBL	Nebulette	0.4561	68
REV1	REV1 DNA directed polymerase	0.4541	55

IMMUNE CELLS

PTCD3 is part of cluster 3 Non-specific - Nuclear processes with confidenceⁱ 0.96
471 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
SBDS	SBDS ribosome maturation factor	0.9762	3
MAN1A2	Mannosidase alpha class 1A member 2	0.9762	3
SMYD2	SET and MYND domain containing 2	0.9762	3
ERG28	Ergosterol biosynthesis 28 homolog	0.9762	3
ZMYND11	Zinc finger MYND-type containing 11	0.9762	3
RPA2	Replication protein A2	0.9762	3
RWDD1	RWD domain containing 1	0.9762	3
PEX12	Peroxisomal biogenesis factor 12	0.9762	3
SSBP1	Single stranded DNA binding protein 1	0.9762	3
ACAT2	Acetyl-CoA acetyltransferase 2	0.9524	3
ZNF331	Zinc finger protein 331	0.9524	3
RASSF7	Ras association domain family member 7	0.9524	3
SSB	Small RNA binding exonuclease protection factor La	0.9524	3
TADA1	Transcriptional adaptor 1	0.9524	3
CCDC127	Coiled-coil domain containing 127	0.9524	3

Adipocytes	15.2 nTPM
Breast	16.8 nTPM
Adipose tissue	13.6 nTPM

Alveolar cells type 1	44.9 nTPM
Lung	44.9 nTPM

Alveolar cells type 2	38.1 nTPM
Lung	38.1 nTPM

Astrocytes	47.7 nTPM
Brain	47.7 nTPM

B-cells	32.2 nTPM
Salivary gland	50.6 nTPM
Lung	40.2 nTPM
Lymph node	38.0 nTPM
Thymus	37.4 nTPM
Stomach	36.7 nTPM
PBMC	33.9 nTPM
Spleen	33.5 nTPM
Adipose tissue	33.3 nTPM
Bone marrow	30.3 nTPM
Esophagus	29.5 nTPM
Kidney	26.0 nTPM
Liver	24.2 nTPM
Skin	5.1 nTPM

Ciliated cells	26.2 nTPM
Fallopian tube	27.0 nTPM
Lung	26.6 nTPM
Bronchus	25.6 nTPM
Endometrium	25.5 nTPM

Club cells	27.1 nTPM
Bronchus	28.6 nTPM
Lung	27.7 nTPM
Prostate	24.9 nTPM

Dendritic cells	33.1 nTPM
Adipose tissue	44.6 nTPM
PBMC	21.6 nTPM

Endothelial cells	22.4 nTPM
Heart muscle	40.3 nTPM
Salivary gland	30.5 nTPM
Prostate	24.8 nTPM
Lung	24.5 nTPM
Ovary	24.5 nTPM
Pancreas	23.3 nTPM
Thymus	22.6 nTPM
Skeletal muscle	22.3 nTPM
Vascular	22.2 nTPM
Endometrium	21.4 nTPM
Fallopian tube	20.3 nTPM
Testis	20.1 nTPM
Tongue	19.6 nTPM
Liver	18.9 nTPM
Breast	18.5 nTPM
Placenta	18.2 nTPM
Skin	16.6 nTPM
Esophagus	15.1 nTPM

Enteroendocrine cells	27.3 nTPM
Colon	34.5 nTPM
Rectum	33.5 nTPM
Small intestine	13.7 nTPM

Fibroblasts	25.3 nTPM
Heart muscle	46.0 nTPM
Salivary gland	33.8 nTPM
Liver	30.8 nTPM
Skeletal muscle	29.4 nTPM
Lung	28.0 nTPM
Thymus	27.4 nTPM
Vascular	26.2 nTPM
Fallopian tube	23.7 nTPM
Prostate	22.4 nTPM
Breast	22.4 nTPM
Placenta	21.1 nTPM
Stomach	20.2 nTPM
Esophagus	19.9 nTPM
Adipose tissue	19.4 nTPM
Pancreas	18.0 nTPM
Skin	16.1 nTPM

Granulocytes	27.8 nTPM
Tongue	34.0 nTPM
Fallopian tube	25.9 nTPM
Lung	23.7 nTPM

Intestinal goblet cells	24.6 nTPM
Rectum	28.5 nTPM
Colon	26.1 nTPM
Small intestine	19.1 nTPM

Lymphatic endothelial cells	17.3 nTPM
Fallopian tube	18.2 nTPM
Ovary	16.4 nTPM

Macrophages	19.7 nTPM
Salivary gland	31.4 nTPM
Tongue	29.2 nTPM
Lung	27.2 nTPM
Vascular	25.9 nTPM
Prostate	25.6 nTPM
Endometrium	22.1 nTPM
Testis	21.1 nTPM
Breast	20.6 nTPM
Stomach	18.0 nTPM
Fallopian tube	17.7 nTPM
Thymus	17.5 nTPM
Bone marrow	17.2 nTPM
Kidney	16.8 nTPM
Skeletal muscle	16.8 nTPM
Adipose tissue	16.3 nTPM
Esophagus	15.4 nTPM
Spleen	14.0 nTPM
Skin	12.3 nTPM
Pancreas	8.2 nTPM

Basal prostatic cells	22.7 nTPM
Prostate	22.7 nTPM

Basal respiratory cells	28.8 nTPM
Bronchus	28.8 nTPM

Basal squamous epithelial cells	31.5 nTPM
Esophagus	31.5 nTPM

Bipolar cells	56.6 nTPM
Eye	56.6 nTPM

Paneth cells	15.6 nTPM
Rectum	22.1 nTPM
Small intestine	13.8 nTPM
Colon	10.9 nTPM

Plasma cells	26.2 nTPM
Thymus	41.3 nTPM
Salivary gland	30.9 nTPM
Stomach	30.2 nTPM
Liver	28.5 nTPM
Spleen	27.9 nTPM
Fallopian tube	27.3 nTPM
Bone marrow	18.1 nTPM
Esophagus	5.2 nTPM

Schwann cells	23.9 nTPM
Vascular	29.8 nTPM
Esophagus	24.0 nTPM
Adipose tissue	18.0 nTPM

Serous glandular cells	24.7 nTPM
Salivary gland	27.2 nTPM
Tongue	22.1 nTPM

Smooth muscle cells	20.6 nTPM
Salivary gland	27.4 nTPM
Placenta	25.9 nTPM
Tongue	25.4 nTPM
Skeletal muscle	25.2 nTPM
Vascular	24.3 nTPM
Prostate	22.5 nTPM
Thymus	22.3 nTPM
Liver	20.0 nTPM
Endometrium	19.8 nTPM
Fallopian tube	19.5 nTPM
Adipose tissue	19.4 nTPM
Ovary	19.4 nTPM
Breast	17.7 nTPM
Skin	16.7 nTPM
Esophagus	13.2 nTPM
Lung	10.6 nTPM

Suprabasal keratinocytes	26.5 nTPM
Skin	27.9 nTPM
Tongue	25.2 nTPM

T-cells	33.2 nTPM
Salivary gland	49.8 nTPM
Prostate	42.9 nTPM
Lung	40.5 nTPM
Thymus	38.9 nTPM
Lymph node	37.2 nTPM
Vascular	36.6 nTPM
Skeletal muscle	36.3 nTPM
Tongue	36.3 nTPM
Adipose tissue	34.7 nTPM
Fallopian tube	34.4 nTPM
PBMC	34.3 nTPM
Esophagus	34.1 nTPM
Stomach	33.7 nTPM
Liver	33.4 nTPM
Breast	31.0 nTPM
Spleen	29.2 nTPM
Bone marrow	28.3 nTPM
Endometrium	28.2 nTPM
Skin	21.7 nTPM
Colon	21.4 nTPM
Kidney	13.3 nTPM

Undifferentiated cells	40.4 nTPM
Rectum	44.7 nTPM
Colon	41.4 nTPM
Small intestine	35.2 nTPM

Amygdala excitatory	68.1 nTPM
Hypothalamus	74.4 nTPM
Amygdala	71.7 nTPM
Hippocampus	71.7 nTPM
Cerebral cortex	67.7 nTPM
Thalamus	63.1 nTPM
Basal ganglia	60.2 nTPM

Astrocyte	84.0 nTPM
Amygdala	96.0 nTPM
Thalamus	93.1 nTPM
Cerebral cortex	92.0 nTPM
Midbrain	89.7 nTPM
Hippocampus	87.8 nTPM
Cerebellum	85.8 nTPM
Basal ganglia	81.5 nTPM
Pons	81.4 nTPM
Hypothalamus	76.8 nTPM
Spinal cord	71.8 nTPM
Medulla oblongata	67.6 nTPM

Bergmann glia	68.1 nTPM
Pons	76.2 nTPM
Cerebellum	68.5 nTPM
Medulla oblongata	59.7 nTPM

Central nervous system macrophage	67.4 nTPM
Amygdala	82.6 nTPM
Hippocampus	76.0 nTPM
Cerebellum	71.2 nTPM
Midbrain	70.4 nTPM
Hypothalamus	69.8 nTPM
Cerebral cortex	66.2 nTPM
Thalamus	65.5 nTPM
Pons	63.0 nTPM
Basal ganglia	60.4 nTPM
Medulla oblongata	59.3 nTPM
Spinal cord	56.5 nTPM

Cerebellar inhibitory	64.6 nTPM
Cerebellum	68.8 nTPM
Midbrain	67.8 nTPM
Spinal cord	63.2 nTPM
Pons	63.1 nTPM
Medulla oblongata	60.2 nTPM

Cge interneuron	67.5 nTPM
Hypothalamus	74.5 nTPM
Amygdala	72.5 nTPM
Cerebral cortex	68.2 nTPM
Hippocampus	65.8 nTPM
Basal ganglia	64.9 nTPM
Midbrain	64.5 nTPM
Thalamus	62.0 nTPM

Choroid plexus epithelial cell	80.3 nTPM
Basal ganglia	125.1 nTPM
Medulla oblongata	91.1 nTPM
Hippocampus	55.5 nTPM
Thalamus	49.3 nTPM

Committed oligodendrocyte precursor	68.7 nTPM
Hypothalamus	90.8 nTPM
Thalamus	77.9 nTPM
Hippocampus	77.1 nTPM
Cerebral cortex	70.3 nTPM
Amygdala	69.4 nTPM
Midbrain	68.0 nTPM
Medulla oblongata	65.8 nTPM
Cerebellum	65.0 nTPM
Basal ganglia	64.1 nTPM
Spinal cord	62.5 nTPM
Pons	44.3 nTPM

Deep-layer corticothalamic and 6b	67.6 nTPM
Midbrain	69.9 nTPM
Cerebral cortex	69.8 nTPM
Hippocampus	67.5 nTPM
Hypothalamus	67.5 nTPM
Amygdala	65.9 nTPM
Basal ganglia	65.1 nTPM

Deep-layer intratelencephalic	67.1 nTPM
Hypothalamus	72.7 nTPM
Amygdala	70.4 nTPM
Cerebral cortex	67.4 nTPM
Basal ganglia	63.3 nTPM
Hippocampus	61.6 nTPM

Deep-layer near-projecting	74.0 nTPM
Amygdala	84.8 nTPM
Cerebral cortex	78.7 nTPM
Basal ganglia	74.5 nTPM
Hypothalamus	71.5 nTPM
Hippocampus	60.5 nTPM

Eccentric medium spiny neuron	80.8 nTPM
Thalamus	86.1 nTPM
Hypothalamus	85.0 nTPM
Basal ganglia	84.5 nTPM
Cerebral cortex	80.5 nTPM
Amygdala	78.8 nTPM
Hippocampus	69.6 nTPM